Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “crystal structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed1977

Molecular structure of thyroxine analogues. Crystal structure of 3,5,3'-triiodothyroacetic and 3,5,3',5'-tetraoiodothyroacetic acid N-diethanolamine (1:1) complexes.

Crystallographic data demonstrated that conformations of thyroid hormones and their derivatives in which the phenyl rings are either skewed (phi,phi'; +/-90,0 degrees) or twist-skewed (phi,phi'; +/-108, +/-28 degrees) are energetically favored. Acetic acid metabolites are consistently observed in the skewed conformation whereas their parent hormones are observed in the twist-skewed conformation. These preferences are manifestations of long-range conformational transmission and together with plasma protein binding data may indicate a site-specific preference for the skewed vs. twist-skewed conformation. These findings result in part from the crystal structure determinations of the N-diethanolamine (1:1) complexes of the active thyroxine metabolites 3,5,3'-triiodothyroacetic acid (T3AA) and 3,5,3'5'-tetraiodothyroacetic acid (T4AA) which are reported here. The conformation of the 3'-iodine in the hypocholestermic agent T3AA is distal, the biologically preferred conformation, and the overall conformation of T3AA is transoid, while that of T4AA is cisoid.

Chemical Phenomena↗
PubMed1979

Crystal structure analysis of the tetragonal crystal form are preliminary molecular model of pig-heart citrate synthase.

The crystal structure of pig heart citrate synthase was analyzed at 0.35-nm resolution. Chain tracing was possible and an initial molecular model constructed. The dimensions of the dimer molecule (located on a crystallographic diad) are 7.5 x 6.0 x 9.0 nm. The chain folding is characterized by the predominance of helices and the absence of sheet structure. The electron density accounts for 355 residues per monomer, so that about 80 residues must be disordered in the crystal. The disordered segment in probably N-terminal. The ordered part consists of two closely associated domains, a large domain with 300 residues and a C-terminal domain of 55 residues consisting of 3(anti)parallel helices. The large domain is built from 12 helical segments, some of which are buried in the interior of the molecule. Inhibitor binding studies with citrate and CoA revealed citrate binding sites but showed no electron density for CoA. It is suggested that CoA binds to the disordered, flexible N-terminal domain. Experiments of limited proteolysis with trypsin showed that under conditions a segment of Mr 9000 is cleaved off selectively. The remaining 35 000-Mr part is dimeric.

Animals↗
PubMed1977

5-Nitrouridine-monohydrate: crystal structure and conformation.

The crystal structure of 5-nitrouridine was determined by X-ray analysis. The pyrimidine ring is slightly non-planar, showing a shallow boat conformation. The nitro group has no influence on the C4 - O4 bond length as compared to uridine. The ribose shows the C3'-endo conformation and the base is in the anti orientation to the sugar with a torsion angle of 25.6 degrees. This conformation is stabilized by a hydrogen bond from the base to the ribosyl moiety (H6 ... 05'). Stacking interactions between neighboring bases are almost negligible in the crystal. A water molecule is involved in a bifurcated donating hydrogen bond to 04 and to 052 of the nitro group of the one base and an accepting bond from the H3 of the other base. Two more hydrogen bonds are formed between the water molecule and the ribose. The structural aspects of 5-nitrouridine are discussed with respect to the special stacking features found for 5-nitro-1-(beta-D-ribosyluronic acid)-uracil monohydrate in the crystal (1).

Models, Chemical↗
PubMed1976

Aggregation of acridine orange: crystal structure of acridine orange tetrachlorozincate 2C17H19N3-2HCl-ZnCl2-CH3COOH.

The crystal structure of the biological stain, "acridine orange," has been determined. This compound, when crystallized from ethanol, is shown to be a zinc chloride double salt of acridine orange, containing, in addition, acetic acid of crystallization. These additional components are residuals from the method of preparation of acridine orange. This complex, 2 acridine orange-2HCl-ZnCl2-CH3COOH, (2C17H19N3-2HCl-ZnCl2-CH3COOH) crystallizes in the monoclinic space group P21, a = 9.965 (2), b = 21.507 (6), c = 9.645 (2) A, beta = 113.98 degrees (2), V = 1888.7 (8) A3, FW = 800.0, Z = 2, DX = 1.41 g-cm-3, Dobs = 1.43 (9) g-cm-3. Three-dimensional diffraction data were collected with CuKalpha radiation, and the structure refined to R = 0.065 for 1885 observed reflections. In the crystal structure hydrogen bonds are formed, via the protonated nitrogen atom of the central rings of two acridine orange cations, to two chloride ions in a ZnCl42- tetrahedral grouping. These two acridine orange molecules are stacked in parallel planes, approximately 3.4 A apart, with the long axes of the ring systems inclined at 26.5 to each other. Thus an apparent dimerization of the acridine, orange is facilitated by the anions present, resulting in the complex studied. The two -N(CH3)2 groups of each acridine orange molecule are not protonated in this crystalline form. The mode of molecular packing found here may be relevant to models for the external stacking of acridine orange around a DNA molecule. The importance of removing any zinc salt from acridine orange preparations prior to aggregation studies is stressed.

Acridines↗
PubMed1979

Structure of a Gla-containing dipeptide. The crystal structure of (+/-)-N-carbobenzoxy-(gamma,gamma'-DI-tertbutyl)-gamma-carboxyglutamylglycine ethyl ester.

The crystal and molecular structure of a dipeptide containing a blocked gamma-carboxyglutamyl (Gla) residue is presented. Two intermolecular hydrogen bonds link the amides with carbonyl groups in the dipeptide backbone, but the protected gamma-carboxy groups on the modified glutamic acid are not hydrogen bonded.

1-Carboxyglutamic Acid↗
PubMed1977

Nucleic acid binding drugs. Part IV. The crystal structure of the anti-cancer agent daunomycin.

The crystal structure has been determined of the anti-cancer drug daunomycin, as the hydrochloride monohydrate pyridine salt. The overall structure, previously determined by X-ray analysis of an N-bromoacetyl derivative (Anguili, R., Foresti, E., Riva Di Sanserverino, L., Isaacs, N.W., Kennard, O., Motherwell, W.D.S., Wampler, D.L. and Arcamone, F. (1971) Nat. New Biol. 234, 78-80) has been confirmed, although substantial conformational differences are observed. The conformation described here is very similar to that found for the related drug carminomycin I (Wani, M.C., Taylor, H.L., Wall, M.E., McPhaill, A.T. and Onan, K.D. (1975) J. Am. Chem. Soc. 97, 5955-5956; Pettit, G.R., Einck, J.J., Herald, C.L., Ode, R.H. Von Dreele, R.B., Brown, P., Brazhnikova, M.G. and Gause, G.F. (1975) J. Am. Chem. Soc. 97, 7387-7388); it is suggested that this represents a significantly stable molecular conformation; an intramolecular C(7)...O(9) hydrogen bond is invoked to account for this. This conformation is likely to be at least close to that of daunomycin when bound to DNA.

Computers↗
PubMed1979

Solution of conformation and crystal structure of methyl 3,6-dideoxy-beta-D-ribohexopyranoside, an immunodominant sugar of O-antigens.

The crystal structure of methyl 3,6-dideoxy-beta-D-ribohexopyranoside monohydrate was determined by direct methods. Crystals are monoclinic, space group P2(1), with cell dimensions a=9.089(1), b=7.668(1), c=6.956(1) A, beta=101.12 degrees. The molecule adopts the 1C1 chair conformation. The same conformation was also found in both aqueous and chloroform solutions. The pyranose ring is only slightly distorted, and the consequences of this observation on antigen structure are discussed.

Antigens, Bacterial↗
PubMed1977

Crystal structure of a protein proteinase inhibitor, Streptomyces subtilisin inhibitor, at 2.3 angstrom resolution.

The crystal structure of a protein proteinase inhibitor, Streptomyces subtilisin inhibitor which strongly inhibits bacterial alkaline proteinases, was determined at 2.3 angstrom resolution. The subunit (molecular weight, 11,485) of this dimeric molecule has a unique fold of polypeptide chain with a five-fold anti-parallel beta-sheet structure (about 21% of the 113 amino acid residues) and two small segments of alpha-helices (about 16%). The region around the apparent reactive site, Met(73)-Val(74), is held tight by a combination of various structural features. The conformation of this region seems to have close similarity to that found in substrate analogues of low molecular weight bound to subtilisin BPN'.

Crystallography↗
PubMed1977

The crystal structure of 3-hydroxy-3-isobutyl-2-pyrrolidone-5-carboxylic acid, lactam of 4-hydroxy-4-isobutylglutamic acid from Reseda odorata L.

The relative configuration of 3-hydroxy-3-isobutyl-2-pyrrolidone-5-carboxylic acid has been determined by an X-ray crystal structure analysis. The compound crystallized in space group P212121 with two molecules in the asymmetric unit. a=16.023(3) A, b=19.349(7) A, c=6.9053(16) A. The structure was solved by direct methods using MULTAN and refined by full-matrix least-squares technique to an R of 0.137 for 645 diffractometer-collected intensities. The absolute configurations of the title compounds were deduced; the configuration of the amino acid and the lactam are 2(S), 4(S) and 3(S), 5(S), respectively.

Chemical Phenomena↗
PubMed1978

Crystal structure of a protein proteinase inhibitor, SSI (Streptomyces subtilisin inhibitor), at 4 A resolution.

The crystal structure of a protein proteinase inhibitor, SSI (Streptomyces subtilisin inhibitor), which strongly inhibits bacterial alkaline proteinases specifically, was determined at 4 A resolution using four heavy-atom derivatives. The SSI molecule can be described as an ellipsoid of about 30 X 40 X 65 A composed of two identical subunits each having dimensions of about 35 X 25 X 40 A and a molecular weight of 11,483. The subunit has an extensive beta-sheet structure, but no long alpha-helices are present. Based on the binding sites of platinum reagents known to form coordination complexes with methionine, it is speculated that the P1 residue, Met 73, of the reactive site is at the protruding edge of the subunit. At the subunit-subunit interface, a beta-sheet of one subunit is stacked on top of the corresponding beta-sheet of the other subunit.

Bacterial Proteins↗
PubMed2026

Crystal structures of Parechovirus A1 3Dpol reveal a mechanism of conformational stabilization in +ssRNA virus RNA-dependent RNA polymerase.

Parechovirus A1 (PeV A1) 3Dpol is an RNA-dependent RNA polymerase responsible for replication of the virus genome. We solved crystal structures of PeV A1 3Dpol structure in complex with GTP and in apo-state at 1.8-2.0 Å resolutions. In the 3Dpol-GTP complex, the conformation of the conserved motif B loop was stabilized by zinc ion coordination by cysteine residues. Apo-state structures of PeV A1 3Dpol showed significant conformational flexibility in the motif B loop, in the absence of zinc. While one of the conformational states of apo-3Dpol was similar to the 3Dpol-GTP complex structure, the alternative apo-3Dpol conformation showed a 4.3 Å movement of the motif B loop out of the active site cavity relative to the complex of 3Dpol with GTP. We propose that PeV A1 3Dpol activity is regulated by conformational stabilization of the motif B loop by zinc coordination.

Crystal structure↗
PubMedDate not supplied

The crystal structure of the pyrimidine analogue calcium 5-ethylidenehydroorotate-1.5 hydrate, a photoproduct of ethylorotate.

X-ray diffraction methods have been employed to establish the crystal structure of a new, unusual pyrimidine analogue, 5-ethylidenehydroorotate, obtained by a photochemical rearrangement of 5-ethylorotate. Crystals of the calcium salt of the title compound are monoclinic, space group Pc, cell constants a=14.631, b=10.038, c=19.168 A, beta=137.7 degrees, and contain four molecules, two cations and three water molecules per asymmetric unit. The structure was solved by direct methods and refined to R=5.2% on the basis of 2653 diffractometer measured data. The four independent molecules represent two pairs of enantiomers with slightly differing conformations linked together by an intricate system of hydrogen bonding and Ca2+-coordination (pentagonal bipyrimidal). The structure of the compound in aqueous medium, established by spectral methods, is the same as that in the crystal.

Models, Molecular↗
PubMed1977

The crystal structure of an acid protease from Rhizopus chinensis at 2.5 A resolution.

This paper contains a preliminary report of the crystal structure of the acid protease from Rhizopus chinensis at 2.5 A resolution. The molecule is bilobal with a large cleft between the lobes. Pepstatin binds in the cleft near the catalytically active Asp-35. The overall folding of the molecule consists primarily of antiparallel beta-strands, there being only four small helices.

Binding Sites↗
PubMed1979

Hydrogen bonds in crystal structures of amino acids, peptides and related molecules.

The results of a survey of 439 hydrogen bonds in 95 recently determined crystal structures of amino acids, peptides and related molecules suggest that the following generalizations hold true for linear (angle X-H---Y greater than 150 degrees) hydrogen bonds. (1) The charge on the acceptor group does not influence the length of a hydrogen bond. (2) For a given acceptor group, the hydrogen bond lengths increase in the order imidazolium N--H less than ammonium N-H less than guanidinium N-H; this order holds true for oxygen anion acceptor groups. Cl-ions and the uncharged oxygen of water molecules. (3) The uncharged imidazole N-H group forms shorter hydrogen than the amide N-H GROUP. (4) The carboxyl O-H groups form shorter hydrogen bonds than other hydroxyl groups. (5) The hydrogen bonds involving a halogen ion are longer than hydrogen bonds with other acceptors when corrected for their longer van der Walls radii. The observed differences between the lengths of hydrogen bonds formed by different donor and acceptor groups in amino acids and peptides, imply differences in the energetics of their formation.

Amino Acids↗
PubMed1978

Crystallization, crystal structure analysis and atomic model of the complex formed by a human Fc fragment and fragment B of protein A from Staphylococcus aureus.

Crystals of the complex formed by human Fc fragment and fragment B (FB) of protein A from Staphylococcus aureus were prepared and the crystal structure determined at high resolution by multiple isomorphous replacement. Phase were improved considerably by combining these phases with calculated phases from the Fc component. FB is a small globular protein built of three parallel helices arranged in a triangular array. It binds by the first two helices of Fc and is attached to segments of CH2 and CH3. The CH3 module is unchanged between complex and Fc fragment crystals, but CH2 changes its position slightly relative to CH3. In addition, the upper third of CH2 is disordered in the complex crystals. Possible sources of this disorder are discussed.

Antigen-Antibody Complex↗